I think it's OK if it's just the precompile helpers.

PS D:\src\chromium\src> Select-String -Pattern '"file":.*third_party/WebKit/Source/build/win/Precompile.cpp' -Path .\out\rel\compile_commands.json

out\rel\compile_commands.json:115035:    "file": "../../third_party/WebKit/Source/build/win/Precompile.cpp"
out\rel\compile_commands.json:116400:    "file": "../../third_party/WebKit/Source/build/win/Precompile.cpp"
out\rel\compile_commands.json:116690:    "file": "../../third_party/WebKit/Source/build/win/Precompile.cpp"

On one hand, this seems like something that we could just ignore.  OTOH, this is probably easy to handle in generate_win_compdb.py (by making sure it only emits unique commands).

Hmmm... interestingly all the 3 commands are unique:

PS D:\src\chromium\src> Select-String -Pattern '"command":.*third_party/WebKit/Source/build/win/Precompile.cpp' -Path .\out\rel\compile_commands.json | % Line | Sort-Object | Get-Unique | Measure-Object | % Count
3

PS D:\src\chromium\src> $xs = Select-String -Pattern '"command":.*third_party/WebKit/Source/build/win/Precompile.cpp' -Path .\out\rel\compile_commands.json | % Line | Sort-Object | Get-Unique 

PS D:\src\chromium\src> Compare-Object -ReferenceObject $xs[0].split(' ') -DifferenceObject $xs[1].split(' ') | Sort-Object InputObject | Format-Table SideIndicator,InputObject

SideIndicator InputObject                                                          
------------- -----------                                                          
<=            /Fdobj/third_party/WebKit/Source/platform/heap/heap_cc.pdb",         
=>            /Fdobj/third_party/WebKit/Source/wtf/wtf_unittests_cc.pdb",          
<=            /Foobj/third_party/WebKit/Source/platform/heap/heap/Precompile.cc.obj
=>            /Foobj/third_party/WebKit/Source/wtf/wtf_unittests/Precompile.cc.obj 
<=            /Fpobj/third_party/WebKit/Source/platform/heap/heap_cc.pch           
=>            /Fpobj/third_party/WebKit/Source/wtf/wtf_unittests_cc.pch            
=>            /wd4068                                                              
=>            /wd4344                                                              
=>            /wd4706                                                              
=>            /wd4800                                                              
=>            -D__STD_C                                                            
=>            -D_CRT_SECURE_NO_DEPRECATE                                           
=>            -D_SCL_SECURE_NO_DEPRECATE                                           
<=            -DBLINK_IMPLEMENTATION=1                                             
<=            -DBLINK_PLATFORM_IMPLEMENTATION=1                                    
<=            -DGR_GL_FUNCTION_TYPE=__stdcall                                      
=>            -DGTEST_HAS_POSIX_RE=0                                               
=>            -DGTEST_LANG_CXX11=1                                                 
<=            -DINSIDE_BLINK                                                       
<=            -DSK_IGNORE_DW_GRAY_FIX                                              
<=            -DSK_IGNORE_LINEONLY_AA_CONVEX_PATH_OPTS                             
<=            -DSK_SUPPORT_GPU=1                                                   
=>            -DUNIT_TEST                                                          
<=            -I../../skia/config                                                  
<=            -I../../skia/ext                                                     
=>            -I../../testing/gmock/include                                        
=>            -I../../testing/gmock_custom                                         
=>            -I../../testing/gtest/include                                        
=>            -I../../third_party/ced/src                                          
<=            -I../../third_party/skia/include/c                                   
<=            -I../../third_party/skia/include/config                              
<=            -I../../third_party/skia/include/core                                
<=            -I../../third_party/skia/include/effects                             
<=            -I../../third_party/skia/include/gpu                                 
<=            -I../../third_party/skia/include/images                              
<=            -I../../third_party/skia/include/lazy                                
<=            -I../../third_party/skia/include/pathops                             
<=            -I../../third_party/skia/include/pdf                                 
<=            -I../../third_party/skia/include/pipe                                
<=            -I../../third_party/skia/include/ports                               
<=            -I../../third_party/skia/include/utils                               
<=            -I../../third_party/skia/src/gpu                                     
<=            -I../../third_party/skia/src/sksl                                    
=>            -I../../third_party/WebKit/Source/wtf/os-win32                       
<=            -I../../v8/include                                                   
<=            -Igen/v8/include                                                     
<=            -Wglobal-constructors                                                

This bug is only responsible for 4 failures (all in irrelevant, precompile files).

D:\src\chromium\src>python tools/clang/scripts/run_tool.py rewrite_to_chrome_style --tool-args=--method-blocklist=d:\scratch\idl_blacklist.txt --all out/rel >run_tool.win.rel.out
...
Processed 30920 files with rewrite_to_chrome_style tool (4 failures) [100.00%]

I wasn't able to reproduce this, so I'm not entirely sure what changed since then. Maybe the changes to generating the compile DB fixed this by accident.